Job ID = 14519846 SRX = SRX9786289 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9868136 spots for SRR13362121/SRR13362121.sra Written 9868136 spots for SRR13362121/SRR13362121.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:49 9868136 reads; of these: 9868136 (100.00%) were paired; of these: 1552990 (15.74%) aligned concordantly 0 times 7043262 (71.37%) aligned concordantly exactly 1 time 1271884 (12.89%) aligned concordantly >1 times ---- 1552990 pairs aligned concordantly 0 times; of these: 75868 (4.89%) aligned discordantly 1 time ---- 1477122 pairs aligned 0 times concordantly or discordantly; of these: 2954244 mates make up the pairs; of these: 1850492 (62.64%) aligned 0 times 911591 (30.86%) aligned exactly 1 time 192161 (6.50%) aligned >1 times 90.62% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 834882 / 8388751 = 0.0995 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 18:06:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:06:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:06:24: 1000000 INFO @ Sat, 15 Jan 2022 18:06:29: 2000000 INFO @ Sat, 15 Jan 2022 18:06:34: 3000000 INFO @ Sat, 15 Jan 2022 18:06:40: 4000000 INFO @ Sat, 15 Jan 2022 18:06:45: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 18:06:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:06:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:06:50: 6000000 INFO @ Sat, 15 Jan 2022 18:06:55: 1000000 INFO @ Sat, 15 Jan 2022 18:06:55: 7000000 INFO @ Sat, 15 Jan 2022 18:07:00: 2000000 INFO @ Sat, 15 Jan 2022 18:07:01: 8000000 INFO @ Sat, 15 Jan 2022 18:07:05: 3000000 INFO @ Sat, 15 Jan 2022 18:07:06: 9000000 INFO @ Sat, 15 Jan 2022 18:07:11: 4000000 INFO @ Sat, 15 Jan 2022 18:07:11: 10000000 INFO @ Sat, 15 Jan 2022 18:07:16: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:07:17: 11000000 INFO @ Sat, 15 Jan 2022 18:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 18:07:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:07:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:07:22: 6000000 INFO @ Sat, 15 Jan 2022 18:07:22: 12000000 INFO @ Sat, 15 Jan 2022 18:07:24: 1000000 INFO @ Sat, 15 Jan 2022 18:07:27: 7000000 INFO @ Sat, 15 Jan 2022 18:07:27: 13000000 INFO @ Sat, 15 Jan 2022 18:07:29: 2000000 INFO @ Sat, 15 Jan 2022 18:07:33: 8000000 INFO @ Sat, 15 Jan 2022 18:07:34: 14000000 INFO @ Sat, 15 Jan 2022 18:07:35: 3000000 INFO @ Sat, 15 Jan 2022 18:07:38: 9000000 INFO @ Sat, 15 Jan 2022 18:07:39: 15000000 INFO @ Sat, 15 Jan 2022 18:07:40: 4000000 INFO @ Sat, 15 Jan 2022 18:07:44: 10000000 INFO @ Sat, 15 Jan 2022 18:07:44: 16000000 INFO @ Sat, 15 Jan 2022 18:07:46: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 18:07:46: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 18:07:46: #1 total tags in treatment: 7482493 INFO @ Sat, 15 Jan 2022 18:07:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:07:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:07:46: 5000000 INFO @ Sat, 15 Jan 2022 18:07:46: #1 tags after filtering in treatment: 4159166 INFO @ Sat, 15 Jan 2022 18:07:46: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 18:07:46: #1 finished! INFO @ Sat, 15 Jan 2022 18:07:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:07:46: #2 number of paired peaks: 138 WARNING @ Sat, 15 Jan 2022 18:07:46: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 15 Jan 2022 18:07:46: start model_add_line... INFO @ Sat, 15 Jan 2022 18:07:46: start X-correlation... INFO @ Sat, 15 Jan 2022 18:07:46: end of X-cor INFO @ Sat, 15 Jan 2022 18:07:46: #2 finished! INFO @ Sat, 15 Jan 2022 18:07:46: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:07:46: #2 alternative fragment length(s) may be 0,57,77,87,112,121,186,211,265,291,297,305,310,350,371,396,411,439,483,496,504,527,549,555,562,589 bps INFO @ Sat, 15 Jan 2022 18:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.05_model.r WARNING @ Sat, 15 Jan 2022 18:07:46: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:07:46: #2 You may need to consider one of the other alternative d(s): 0,57,77,87,112,121,186,211,265,291,297,305,310,350,371,396,411,439,483,496,504,527,549,555,562,589 WARNING @ Sat, 15 Jan 2022 18:07:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:07:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:07:49: 11000000 INFO @ Sat, 15 Jan 2022 18:07:51: 6000000 INFO @ Sat, 15 Jan 2022 18:07:54: 12000000 INFO @ Sat, 15 Jan 2022 18:07:57: 7000000 INFO @ Sat, 15 Jan 2022 18:08:00: 13000000 INFO @ Sat, 15 Jan 2022 18:08:02: 8000000 INFO @ Sat, 15 Jan 2022 18:08:06: 14000000 INFO @ Sat, 15 Jan 2022 18:08:08: 9000000 INFO @ Sat, 15 Jan 2022 18:08:12: 15000000 INFO @ Sat, 15 Jan 2022 18:08:13: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:08:18: 16000000 INFO @ Sat, 15 Jan 2022 18:08:19: 11000000 INFO @ Sat, 15 Jan 2022 18:08:19: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 18:08:19: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 18:08:19: #1 total tags in treatment: 7482493 INFO @ Sat, 15 Jan 2022 18:08:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:08:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:08:19: #1 tags after filtering in treatment: 4159166 INFO @ Sat, 15 Jan 2022 18:08:19: #1 Redundant rate of treatment: 0.44 INFO @ Sat, 15 Jan 2022 18:08:19: #1 finished! INFO @ Sat, 15 Jan 2022 18:08:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:08:19: #2 number of paired peaks: 138 WARNING @ Sat, 15 Jan 2022 18:08:19: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 15 Jan 2022 18:08:19: start model_add_line... INFO @ Sat, 15 Jan 2022 18:08:19: start X-correlation... INFO @ Sat, 15 Jan 2022 18:08:19: end of X-cor INFO @ Sat, 15 Jan 2022 18:08:19: #2 finished! INFO @ Sat, 15 Jan 2022 18:08:19: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:08:19: #2 alternative fragment length(s) may be 0,57,77,87,112,121,186,211,265,291,297,305,310,350,371,396,411,439,483,496,504,527,549,555,562,589 bps INFO @ Sat, 15 Jan 2022 18:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786289/SRX9786289.10_model.r WARNING @ Sat, 15 Jan 2022 18:08:19: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:08:19: #2 You may need to consider one of the other alternative d(s): 0,57,77,87,112,121,186,211,265,291,297,305,310,350,371,396,411,439,483,496,504,527,549,555,562,589 WARNING @ Sat, 15 Jan 2022 18:08:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:08:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:08:24: 12000000 BigWig に変換しました。 /var/spool/uge/at163/job_scripts/14519846: line 297: 128018 Terminated MACS $i /var/spool/uge/at163/job_scripts/14519846: line 297: 128138 Terminated MACS $i /var/spool/uge/at163/job_scripts/14519846: line 297: 128269 Terminated MACS $i ls: cannot access SRX9786289.05.bed: No such file or directory mv: cannot stat ‘SRX9786289.05.bed’: No such file or directory mv: cannot stat ‘SRX9786289.05.bb’: No such file or directory ls: cannot access SRX9786289.10.bed: No such file or directory mv: cannot stat ‘SRX9786289.10.bed’: No such file or directory mv: cannot stat ‘SRX9786289.10.bb’: No such file or directory ls: cannot access SRX9786289.20.bed: No such file or directory mv: cannot stat ‘SRX9786289.20.bed’: No such file or directory mv: cannot stat ‘SRX9786289.20.bb’: No such file or directory